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- PDB-5npk: 1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA -

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Basic information

Entry
Database: PDB / ID: 5npk
Title1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA
Components
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B ...Rossmann fold - #670 / DNA gyrase, subunit A / : / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-94H / Chem-9JN / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å
AuthorsBax, B.D. / Chan, P.F. / Stavenger, R.A.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative Joint Undertaking115583
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Authors: Chan, P.F. / Germe, T. / Bax, B.D. / Huang, J. / Thalji, R.K. / Bacque, E. / Checchia, A. / Chen, D. / Cui, H. / Ding, X. / Ingraham, K. / McCloskey, L. / Raha, K. / Srikannathasan, V. / ...Authors: Chan, P.F. / Germe, T. / Bax, B.D. / Huang, J. / Thalji, R.K. / Bacque, E. / Checchia, A. / Chen, D. / Cui, H. / Ding, X. / Ingraham, K. / McCloskey, L. / Raha, K. / Srikannathasan, V. / Maxwell, A. / Stavenger, R.A.
History
DepositionApr 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Advisory / Category: pdbx_validate_polymer_linkage
Item: _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
b: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
d: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
e: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
f: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,50237
Polymers336,9768
Non-polymers4,52629
Water47,9922664
1
B: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,36517
Polymers168,4884
Non-polymers1,87713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-70 kcal/mol
Surface area56890 Å2
MethodPISA
2
b: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
d: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
e: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
f: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,13720
Polymers168,4884
Non-polymers2,64916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16660 Å2
ΔGint-89 kcal/mol
Surface area57180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.442, 120.680, 168.899
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 8 molecules BDbdEFef

#1: Protein
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A


Mass: 78109.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: gyrB, SA0005, gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3
#2: DNA chain
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 6134.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 8 types, 2693 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-94H / ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide


Mass: 362.448 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H18N4OS
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-9JN / ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide


Mass: 362.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N4OS
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2664 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 11 % PEG 5000 MME, 150 mM Bis-Tris pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.763
11h,-k,-l20.237
ReflectionResolution: 1.98→19.97 Å / Num. obs: 245600 / % possible obs: 98.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.043 / Rrim(I) all: 0.082 / Net I/σ(I): 11.8 / Num. measured all: 891144 / Scaling rejects: 3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.673 / CC1/2: 0.542 / Rpim(I) all: 0.533 / Rrim(I) all: 0.866 / % possible all: 89.9

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.98→19.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.511 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.027 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1832 12302 5 %RANDOM
Rwork0.1538 ---
obs0.1552 233267 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 207.01 Å2 / Biso mean: 37.577 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1--13.6 Å20 Å22.91 Å2
2--23.29 Å20 Å2
3----9.69 Å2
Refinement stepCycle: final / Resolution: 1.98→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21160 1483 304 2683 25630
Biso mean--43.18 45.7 -
Num. residues----2767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01924907
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.91334073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52452904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51523.4431121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.678154207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.68515265
X-RAY DIFFRACTIONr_chiral_restr0.1070.23688
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118853
LS refinement shellResolution: 1.978→2.029 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 767 -
Rwork0.248 15099 -
all-15866 -
obs--86.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.068-0.39980.37270.69470.20640.56060.06850.1476-0.2185-0.1259-0.0135-0.07760.0408-0.0184-0.0550.2068-0.00610.0020.1466-0.07030.205228.683516.7829-20.5654
20.4380.125-0.06130.5134-0.16710.19870.0335-0.07460.09040.02420.00360.0664-0.00860.0103-0.03710.1579-0.00040.00520.1714-0.01180.163514.810946.57764.8355
32.227-0.89661.27640.7269-1.12671.7981-0.0602-0.0533-0.13830.04310.0850.00590.0029-0.1938-0.02470.2293-0.03250.03150.2826-0.01220.072116.322742.47937.0023
43.0647-0.6393-0.07040.4643-0.16160.4704-0.1373-0.1519-0.13950.0589-0.0226-0.02530.1045-0.06250.15980.24140.00370.02440.20450.01390.089533.6336.179248.5773
51.0372-0.7263-0.54740.77460.4350.9692-0.0350.0368-0.30860.0092-0.00330.12910.0928-0.06260.03830.1788-0.0297-0.03740.1448-0.02150.21479.84518.9178-12.3642
61.1721-0.4685-0.290.6515-0.06780.57360.10810.15940.24-0.1075-0.1002-0.0056-0.05830.0258-0.00790.20260.04330.04320.11030.08280.215247.458761.3118-21.8067
70.5601-0.17740.05550.3352-0.00110.11950.0165-0.0328-0.0084-0.021-0.0073-0.0218-0.0074-0.0003-0.00920.162-0.00040.00750.16350.00510.162864.048531.62292.314
81.01390.0194-1.06560.96820.51431.4576-0.0091-0.02930.08120.12530.1288-0.1108-0.00060.067-0.11970.18820.0271-0.05420.2168-0.03340.0865.586236.172434.0943
92.1434-0.8542-0.31832.10040.50990.4784-0.1432-0.14410.07230.17560.14250.0409-0.01770.10970.00070.21910.0478-0.02710.20430.0130.044249.715642.073347.7654
101.0746-1.03231.05760.9986-1.03751.3172-0.04030.08450.34190.0202-0.1051-0.3344-0.04640.10610.14540.1785-0.00690.08070.12230.07250.328667.21159.0168-15.5985
110.3779-0.2649-0.11490.26540.19920.3356-0.03520.06170.0365-0.07770.01550.0002-0.05840.03460.01970.2431-0.0229-0.03780.19030.0180.168616.428639.0466-16.5471
120.64640.082-0.04570.0657-0.12930.2852-0.01870.09810.0791-0.07750.02230.00230.145-0.0195-0.00360.23750.01830.04490.18610.01830.134459.293538.7823-18.8618
130.45610.2297-0.26681.3752-0.00250.3719-0.01640.05640.0715-0.21550.04680.10680.0625-0.0399-0.03040.2092-0.0069-0.05220.12490.03340.18714.36666.6439-22.4056
141.1961-0.2046-0.07431.3182-0.0621.1955-0.01020.2456-0.2355-0.284-0.00150.00550.175-0.07870.01170.26550.00440.00750.2021-0.09160.172261.683510.8984-24.2854
151.0029-0.3394-0.32960.6397-0.15990.5290.03060.11860.1764-0.1309-0.00760.11890.02730.0282-0.0230.18070.0046-0.0520.15330.04820.19785.155761.554563.37
160.4174-0.01690.15520.38570.04270.27290.03170.0005-0.04920.00850.0235-0.0320.01270.0022-0.05520.15090.0208-0.04220.1692-0.01480.156919.012231.982189.3871
173.0027-0.1268-1.6831.26411.19611.9670.00390.00110.01930.09320.0226-0.02670.0257-0.0064-0.02650.18830.0344-0.06240.22780.00560.065217.253336.2561121.3563
182.601-0.5667-0.13660.792-0.07060.4289-0.0643-0.19260.1190.12610.0159-0.0704-0.0879-0.00950.04850.20.0686-0.05010.2382-0.04270.04950.080442.3898133.1677
191.0806-0.68270.28090.513-0.3680.5981-0.01660.02140.2580.0031-0.0038-0.1391-0.04670.09570.02040.164-0.02080.00050.1890.00450.205423.642959.933471.5485
201.079-0.57250.20820.655-0.14030.76520.11710.0897-0.1984-0.1453-0.06060.0320.14430.0077-0.05650.24840.0158-0.09780.1-0.04450.1909-13.57917.00862.6381
210.6644-0.15640.09030.2613-0.0510.15650.0087-0.14880.0055-0.03340.01880.0060.0158-0.0288-0.02750.1388-0.0042-0.04240.20730.00090.1367-30.089146.903986.5013
220.1702-0.40060.28171.5738-0.2631.3902-0.06980.0443-0.03020.220.2044-0.0041-0.0546-0.0816-0.13460.13950.03330.0390.42750.03640.0555-31.662643.0994118.5863
232.7578-0.3960.22771.20210.03010.7512-0.1388-0.0766-0.0580.18560.2079-0.07290.0778-0.1104-0.06910.19830.0856-0.00350.2791-0.00510.013-16.149936.6909132.2592
241.0478-0.9333-1.01912.17131.4771.3523-0.0622-0.0205-0.2890.0045-0.0970.38850.1391-0.0780.15910.1985-0.0614-0.14690.15170.0190.3615-33.596319.407268.642
250.2510.09540.21520.06780.07630.1878-0.04420.0386-0.0227-0.0830.05360.0144-0.01380.0342-0.00940.2312-0.00570.00720.2061-0.01650.15813.186738.474367.3832
260.3299-0.0907-0.04680.04170.04590.11370.02740.0025-0.0334-0.05310.00730.0147-0.0385-0.0015-0.03470.2125-0.0008-0.0760.18380.00020.1231-22.478940.464765.5166
271.5246-0.2573-0.09011.985-0.25691.55010.04440.3106-0.3046-0.33410.1038-0.10190.179-0.0334-0.14820.25360.0171-0.04690.2199-0.1470.158819.762211.341662.6375
280.67240.00820.01960.72380.13440.0807-0.08020.09860.1077-0.1671-0.01130.01120.00370.02270.09140.234-0.0122-0.05540.1680.03030.2034-27.658766.580259.0685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B417 - 608
2X-RAY DIFFRACTION1B701 - 714
3X-RAY DIFFRACTION2A29 - 244
4X-RAY DIFFRACTION2A328 - 369
5X-RAY DIFFRACTION2A461 - 491
6X-RAY DIFFRACTION3A370 - 379
7X-RAY DIFFRACTION3A445 - 460
8X-RAY DIFFRACTION4A380 - 444
9X-RAY DIFFRACTION5A10 - 28
10X-RAY DIFFRACTION5B609 - 641
11X-RAY DIFFRACTION6D417 - 608
12X-RAY DIFFRACTION6D701 - 714
13X-RAY DIFFRACTION7C29 - 244
14X-RAY DIFFRACTION7C328 - 369
15X-RAY DIFFRACTION7C461 - 491
16X-RAY DIFFRACTION8C370 - 379
17X-RAY DIFFRACTION8C445 - 460
18X-RAY DIFFRACTION9C380 - 444
19X-RAY DIFFRACTION10C10 - 28
20X-RAY DIFFRACTION10D609 - 641
21X-RAY DIFFRACTION11E-8 - -1
22X-RAY DIFFRACTION11F5 - 12
23X-RAY DIFFRACTION12E4 - 12
24X-RAY DIFFRACTION12F-8 - -1
25X-RAY DIFFRACTION13A245 - 327
26X-RAY DIFFRACTION14C245 - 327
27X-RAY DIFFRACTION15b417 - 608
28X-RAY DIFFRACTION16a29 - 244
29X-RAY DIFFRACTION16a328 - 369
30X-RAY DIFFRACTION16a461 - 490
31X-RAY DIFFRACTION17a370 - 379
32X-RAY DIFFRACTION17a445 - 460
33X-RAY DIFFRACTION18a380 - 444
34X-RAY DIFFRACTION19a8 - 28
35X-RAY DIFFRACTION19b609 - 640
36X-RAY DIFFRACTION20d417 - 608
37X-RAY DIFFRACTION21c29 - 244
38X-RAY DIFFRACTION21c328 - 369
39X-RAY DIFFRACTION21c461 - 490
40X-RAY DIFFRACTION22c370 - 379
41X-RAY DIFFRACTION22c445 - 460
42X-RAY DIFFRACTION23c380 - 444
43X-RAY DIFFRACTION24c10 - 28
44X-RAY DIFFRACTION24d609 - 640
45X-RAY DIFFRACTION25e-8 - -1
46X-RAY DIFFRACTION25f1 - 12
47X-RAY DIFFRACTION26e1 - 12
48X-RAY DIFFRACTION26f-8 - 1
49X-RAY DIFFRACTION27a245 - 327
50X-RAY DIFFRACTION28c245 - 327

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